The long-term accumulation of heavy metals in forest soil organic layers may adversely affect soil microorganisms. The objectives of the study were to assess the effects of high contents of Cu and Zn on the soil microbial communities and their tolerance to metal pollution. Several microbial indices such as microbial biomass (C-mic), the basal soil respiration (BAS), the community level physiological profiles (CLPP) and the pollution-induced community tolerance (PICT) approach, based on Biolog (R) EcoPlate assay, were used. The soil organic layer samples were taken in the Cu-polluted (CuP), Zn-polluted (ZnP) and unpolluted (UP) Scots pine forests. Despite very high total heavy metal concentrations in soils C-mic, BAS and CLPPs at the polluted sites did not differ from those at the UP sites. A damaging effect of heavy metals was detected only by the tolerance measurements with Biolog (R) plates. PICT to Cu at the CuP sites was found for five substrates. At the ZnP sites significant PICT to Zn was found for 10 out of 31 substrates. Furthermore, the CuP samples exhibited lower resistance to Zn and the ZnP samples to Cu compared with the UP samples, indicating that at the polluted sites microbial resistance to additional stress caused by another metal was decreased. Since the tolerance measurements using Biolog (R) assay appeared to be more sensitive than other methods used, we concluded that this approach could be useful in environmental risk assessment.